Nitro.knit

suppressPackageStartupMessages({
library(tidyverse)
library(plotly)
library(treeio)
library(ggtree)
library(ggtreeExtra)
library(svglite)
  })

BGC table for Myxococcota

Rscript notebook/bgc_table.R \
  --antismash_dir  ~/p__Nitrospirota_all/antismash/6.0.1/ \
  --bigscape_dir ~/p__Nitrospirota_all/p__Nitrospirota_all_antismash_6.0.1/network_files/2022-02-01_16-12-56_glocal_p__Nitrospirota_all_antismash_6.0.1/ \
  --output tables/p__Nitrospirota_all_bgcs.csv

## # A tibble: 7,699 × 9
##    bgc_id         GCF   genome_id contig  start    end product contig_edge class
##    <chr>          <chr> <chr>     <chr>   <dbl>  <dbl> <chr>   <lgl>       <chr>
##  1 BBCX01000006.… 0;28… GCA_0013… BBCX0… 103791 119963 betala… TRUE        Othe…
##  2 BDSY01000037.… 2327  GCA_0028… BDSY0…  18239  39643 ranthi… FALSE       RiPPs
##  3 BDSY01000065.… 2326  GCA_0028… BDSY0…      0  18215 ranthi… TRUE        RiPPs
##  4 BDSZ01000026.… 13    GCA_0028… BDSZ0…   8603  49803 ladder… FALSE       Othe…
##  5 BDSZ01000032.… 14    GCA_0028… BDSZ0…   1097  43731 NRPS-l… FALSE       NRPS 
##  6 BDSZ01000042.… 5     GCA_0028… BDSZ0…      0  20604 ladder… TRUE        Othe…
##  7 BDTA01000096.… 16    GCA_0028… BDTA0…  18335  39755 ranthi… FALSE       RiPPs
##  8 BDTA01000122.… 15    GCA_0028… BDTA0…  47296  70788 ladder… TRUE        Othe…
##  9 BDTB01000167.… 8;23… GCA_0028… BDTB0…      0   7268 ladder… TRUE        Othe…
## 10 BDTC01000008.… 9     GCA_0028… BDTC0…      0  21965 NRPS;T… TRUE        PKS-…
## # … with 7,689 more rows

Genome table for Myxococcota

## # A tibble: 317 × 11
##    genome_id       total_bgcs bgcs_on_contig_edge gtdb_taxonomy   assembly_level
##    <chr>                <dbl>               <dbl> <chr>           <chr>         
##  1 GCA_016706135.1          9                   1 d__Bacteria;p_… Contig/Scaffo…
##  2 GCA_016709365.1         10                   0 d__Bacteria;p_… Contig/Scaffo…
##  3 GCA_016712165.1         10                   0 d__Bacteria;p_… Contig/Scaffo…
##  4 GCA_016711755.1          9                   1 d__Bacteria;p_… Contig/Scaffo…
##  5 GCA_016715825.1          9                   0 d__Bacteria;p_… Contig/Scaffo…
##  6 GCA_016719745.1         10                   0 d__Bacteria;p_… Contig/Scaffo…
##  7 GCA_016722315.1         10                   0 d__Bacteria;p_… Contig/Scaffo…
##  8 GCA_016722055.1         11                   0 d__Bacteria;p_… Contig/Scaffo…
##  9 GCA_001567445.1         11                   7 d__Bacteria;p_… Contig/Scaffo…
## 10 GCA_001805205.1          2                   2 d__Bacteria;p_… Contig/Scaffo…
## # … with 307 more rows, and 6 more variables: checkm_completeness <dbl>,
## #   checkm_contamination <dbl>, genome_size <dbl>, ncbi_bioproject <chr>,
## #   mimag_quality <chr>, source <chr>

Customize BiG-SCAPE classes and color palette

bigscape_classes <- c("Terpene",
                      "RiPPs", 
                      "NRPS",
                      "PKS-NRP_Hybrids",
                      "PKSI",
                      "PKSother", 
                      "Saccharides",
                      "Others")                             

my_classes <- c("Terpene", 
                "RiPP", 
                "NRPS", 
                "NRPS-PKS", 
                "PKS", 
                "PKS", 
                "Other", 
                "Other")

my_colors <- c("#ff8800",
               "#20c200",
               "#ff0000",
               "#dd00ff",
               "#0d00ff",
               "#757575")

QC Boxplots for the phylum Nitrospirota

Overview of the phylum Myxococcota. Add number of MAGs per clade

Absence / Presence matrix for f__Nitrospiraceae